Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate PP_3349 PP_3349 3-hydroxyphenylpropionate / 3-hydroxycinnamate:H+ symporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__Putida:PP_3349 Length = 413 Score = 240 bits (613), Expect = 5e-68 Identities = 158/420 (37%), Positives = 216/420 (51%), Gaps = 41/420 (9%) Query: 33 LCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMSAALIGMVFGALGSGPLADRFG 92 LCFL+ L+GLD A G AP +++ + + A LG V SA L+G++ GAL G LADRFG Sbjct: 17 LCFLVALLEGLDLQATGIAAPHMAKAFNLTPAMLGWVFSAGLLGLLPGALIGGWLADRFG 76 Query: 93 RKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGLGAGMPNATTLLSEYTPERLKS 152 RK +L+ AVL+FGGFSL +A+A D LL+ R +TGLGLGA +P L SE PERL+S Sbjct: 77 RKAILIVAVLLFGGFSLGTAHAQTYDSLLIARLMTGLGLGAALPILIALASEAAPERLRS 136 Query: 153 LLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGVLPLLLALVLMVWLPESARFLV 212 V+ +CG LG A I + GW ++ +GG+ P+++A VLM+WL ES F Sbjct: 137 TAVSLTYCGVPLGGAVASLIGMAGV-GDGWRTVFYVGGIAPIVIAFVLMIWLKESQAF-- 193 Query: 213 VRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAARSVFAVIFSGTYGLGTMLLWLTY 272 Q VA+AGS V A +F T+LLW+ Sbjct: 194 ----------------RAQGVAKAGS-----------EGVLAQLFGPQQASRTLLLWVAC 226 Query: 273 FMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFGGVLSAVGVGWAMDRYNPHKVIG 332 F L ++Y+L +WLP+L+ G S QA + LF GG + G MDR + + Sbjct: 227 FFTLTVLYMLLNWLPSLLIGQGFSRPQAGAVQILFNLGGAAGSFLTGRMMDRGFAGRAVL 286 Query: 333 IFYLLAGVFAYAVGQSLGNITVLATLV-LIAGMCVNGAQSAMPSLAARFYPTQGRATGVS 391 I Y AG+ A G L + L L AG C G Q + +LA Y TQ RATG+ Sbjct: 287 IAY--AGMLASLAGLGLSSSFGLMLLAGFTAGYCAIGGQLVLYALAPTLYSTQVRATGLG 344 Query: 392 WMLGIGRFGAILGAWSGATLLGLGWNFEQVLTAL---LVPAALATVGVIVKGLVSHADAT 448 + +GR G++ G + +L G +L A LV AALA + L+ H T Sbjct: 345 ASVAVGRLGSMAGPLAAGQILAAGAGAGGLLMAAAPGLVLAALA-----ARALLKHRTRT 399 Lambda K H 0.325 0.140 0.424 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 519 Number of extensions: 40 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 448 Length of database: 413 Length adjustment: 32 Effective length of query: 416 Effective length of database: 381 Effective search space: 158496 Effective search space used: 158496 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory